Mercurial > repos > gkumar09 > trinityrnaseq_protocol

changeset 27:0bb2b5dc3a53 draft

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Uploaded
author gkumar09
date Fri, 23 Oct 2015 12:07:36 -0400
parents 9af2f4621bb1
children 9b159468135f
files trinityrnaseq_protocol/abundance_estimation_to_matrix.xml trinityrnaseq_protocol/concatanate.xml trinityrnaseq_protocol/concatenate.xml
diffstat 3 files changed, 42 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/trinityrnaseq_protocol/abundance_estimation_to_matrix.xml	Fri Oct 23 12:02:09 2015 -0400
+++ b/trinityrnaseq_protocol/abundance_estimation_to_matrix.xml	Fri Oct 23 12:07:36 2015 -0400
@@ -1,5 +1,6 @@
 <tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="0.0.1">
 
+ <description>Join RSEM estimates from multiple samples into a single matrix</description>
     <requirements>
         <requirement type="package">trinity</requirement>
     </requirements>
--- a/trinityrnaseq_protocol/concatanate.xml	Fri Oct 23 12:02:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<tool id="catbash" name="Concatenate datasets">
-    <description>tail-to-head</description>
-    <command interpreter="python">
-        bash_command_executer.py cat
-        $input1
-        #for $q in $queries
-            ${q.input2}
-        #end for
-        > $out_file1 
-    </command>
-    <inputs>
-        <param name="input1" type="data" label="Concatenate Dataset"/>
-        <repeat name="queries" title="Dataset">
-            <param name="input2" type="data" label="Select" />
-        </repeat>
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="input" metadata_source="input1"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="1.bed"/>
-            <param name="input2" value="2.bed"/>
-            <output name="out_file1" file="cat_wrapper_out1.bed"/>
-        </test>
-        <!--TODO: if possible, enhance the underlying test code to handle this test
-            the problem is multiple params with the same name "input2"
-        <test>
-            <param name="input1" value="1.bed"/>
-            <param name="input2" value="2.bed"/>
-            <param name="input2" value="3.bed"/>
-            <output name="out_file1" file="cat_wrapper_out2.bed"/>
-        </test>
-        -->
-    </tests>
-    <help>
-
-    no help
-
-    </help>
-</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trinityrnaseq_protocol/concatenate.xml	Fri Oct 23 12:07:36 2015 -0400
@@ -0,0 +1,41 @@
+<tool id="catbash" name="Concatenate datasets">
+    <description> concatenate datasets from tail to head</description>
+    <command interpreter="python">
+        bash_command_executer.py cat
+        $input1
+        #for $q in $queries
+            ${q.input2}
+        #end for
+        > $out_file1 
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset"/>
+        <repeat name="queries" title="Dataset">
+            <param name="input2" type="data" label="Select" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed"/>
+            <param name="input2" value="2.bed"/>
+            <output name="out_file1" file="cat_wrapper_out1.bed"/>
+        </test>
+        <!--TODO: if possible, enhance the underlying test code to handle this test
+            the problem is multiple params with the same name "input2"
+        <test>
+            <param name="input1" value="1.bed"/>
+            <param name="input2" value="2.bed"/>
+            <param name="input2" value="3.bed"/>
+            <output name="out_file1" file="cat_wrapper_out2.bed"/>
+        </test>
+        -->
+    </tests>
+    <help>
+
+    no help
+
+    </help>
+</tool>